And so KCC now really is a valuable facet to your AD replication. If you haven't already done so, consider eliminating the aforementioned manual links and allowing the new and improved KCC to resume its responsibility over the AD site topology. Greg Shields, author of the book "Windows Server 2008: What's New, What's Changed" explains that "the KCC automatically applies link costs as part of what it does naturally. In all but the very largest of environments, you should never need to modify anything having to do with the KCC at all."
Using KCC to make your AD topology more efficient is a good start toward deploying Exchange 2007. However, prior to deploying even the first Exchange server, you should officially document your physical sites and subnets and note the current physical and logical links between these sites. Document the site link costs as well. Once you have things documented you want to look for ways to improve your overall infrastructure for superior AD replication topology.
One other enhancement you want to consider before deploying Exchange 2007 is the addition of Global Catalog servers in every site. These are Domain Controllers that retain a copy of every AD object. From an AD perspective, they assist in the logon process and in the search procedures for objects. From an Exchange perspective, they assist in the sending and receiving of mail. So, access to a GC is essential in your Exchange 2007 environment, and one per site is a best practice.
Jumping slightly to the future: You've enhanced your AD infrastructure and deployed your Exchange 2007 servers. Now you wish to make some changes to your messaging environment and perhaps even change those site link costs that KCC calculated.
Why would you want to change those costs? Well, suppose a message has to travel from Site A to Site D. There's no direct connection physically (or logically) but the message can go through Site B or Site C. The route choice is made by adding up the site link costs from A to B to D and the costs from A to C to D. The servers will choose whichever costs less.
There are times, however, when you may feel that you should manually intervene and select a more expensive route; for example, you may not be pleased overall by the speed of messaging based upon costs that are set on the AD side (and perhaps those costs are not functional because they were manually created, rather than making use of the KCC).